0.016964 -0.000000 -0.000000 0.000000 0.011686 -0.000000 0.000000 0.000000 0.021510 0.000000 0.000000 0.000000 Stout, C.D. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.000 90.000 90.000 58.950 85.570 46.490 C50 H64 N6 O10 909.077 benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate TL-3, C2 symmetric inhibitor peptide-like C7 H14 O 114.185 (1S,2S)-2-methylcyclohexanol trans-2-methylcyclohexanol non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C2 H6 O S 78.133 BETA-MERCAPTOETHANOL non-polymer C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C2 H6 O S 78.133 DIMETHYL SULFOXIDE non-polymer C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking K 1 39.098 POTASSIUM ION non-polymer C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N C N 2 N O N 3 N O N 4 N C Y 5 N C Y 6 N C Y 7 N C Y 8 N C Y 9 N C Y 10 N C N 11 N N N 12 S C N 13 N C N 14 N O N 15 N C N 16 N N N 17 S C N 18 N C N 19 N O N 20 N C N 21 N C N 22 N C N 23 R C N 24 N O N 25 S C N 26 N N N 27 N C Y 28 N C Y 29 N C Y 30 N C Y 31 N C Y 32 N C Y 33 N C N 34 N N N 35 S C N 36 R C N 37 N O N 38 N C Y 39 N C Y 40 N C Y 41 N C Y 42 N C Y 43 N C Y 44 N C N 45 N N N 46 S C N 47 N C N 48 N O N 49 N C N 50 N C N 51 N C N 52 N N N 53 S C N 54 N C N 55 N O N 56 N C N 57 N C N 58 N O N 59 N O N 60 N C Y 61 N C Y 62 N C Y 63 N C Y 64 N C Y 65 N C Y 66 N C N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N C N 132 S C N 133 N C N 134 N C N 135 N C N 136 N C N 137 S C N 138 N O N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N N N 154 S C N 155 N C N 156 N O N 157 N C N 158 N O N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N N N 167 S C N 168 N C N 169 N O N 170 N C N 171 N C N 172 N C N 173 N N N 174 N C N 175 N N N 176 N N N 177 N O N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N N N 194 S C N 195 N C N 196 N O N 197 N C N 198 N C N 199 N O N 200 N N N 201 N O N 202 N H N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H N 208 N H N 209 N H N 210 N N N 211 S C N 212 N C N 213 N O N 214 N C N 215 N C N 216 N O N 217 N O N 218 N O N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N C N 227 N C N 228 N O N 229 N S N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N N N 237 R C N 238 N C N 239 N O N 240 N C N 241 N S N 242 N O N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N S N 251 N O N 252 N C N 253 N C N 254 N H N 255 N H N 256 N H N 257 N H N 258 N H N 259 N H N 260 N N N 261 S C N 262 N C N 263 N O N 264 N C N 265 N C N 266 N C N 267 N O N 268 N N N 269 N O N 270 N H N 271 N H N 272 N H N 273 N H N 274 N H N 275 N H N 276 N H N 277 N H N 278 N H N 279 N H N 280 N N N 281 S C N 282 N C N 283 N O N 284 N C N 285 N C N 286 N C N 287 N O N 288 N O N 289 N O N 290 N H N 291 N H N 292 N H N 293 N H N 294 N H N 295 N H N 296 N H N 297 N H N 298 N H N 299 N N N 300 N C N 301 N C N 302 N O N 303 N O N 304 N H N 305 N H N 306 N H N 307 N H N 308 N H N 309 N N N 310 S C N 311 N C N 312 N O N 313 N C Y 314 N C Y 315 N N Y 316 N C Y 317 N C Y 318 N N N 319 N O N 320 N H N 321 N H N 322 N H N 323 N H N 324 N H N 325 N H N 326 N H N 327 N H N 328 N H N 329 N H N 330 N O N 331 N H N 332 N H N 333 N N N 334 S C N 335 N C N 336 N O N 337 S C N 338 N C N 339 N C N 340 N C N 341 N O N 342 N H N 343 N H N 344 N H N 345 N H N 346 N H N 347 N H N 348 N H N 349 N H N 350 N H N 351 N H N 352 N H N 353 N H N 354 N H N 355 N K N 356 N N N 357 S C N 358 N C N 359 N O N 360 N C N 361 N C N 362 N C N 363 N C N 364 N O N 365 N H N 366 N H N 367 N H N 368 N H N 369 N H N 370 N H N 371 N H N 372 N H N 373 N H N 374 N H N 375 N H N 376 N H N 377 N H N 378 N N N 379 S C N 380 N C N 381 N O N 382 N C N 383 N C N 384 N C N 385 N C N 386 N N N 387 N O N 388 N H N 389 N H N 390 N H N 391 N H N 392 N H N 393 N H N 394 N H N 395 N H N 396 N H N 397 N H N 398 N H N 399 N H N 400 N H N 401 N H N 402 N H N 403 N N N 404 S C N 405 N C N 406 N O N 407 N C N 408 N C N 409 N S N 410 N C N 411 N O N 412 N H N 413 N H N 414 N H N 415 N H N 416 N H N 417 N H N 418 N H N 419 N H N 420 N H N 421 N H N 422 N H N 423 N N N 424 S C N 425 N C N 426 N O N 427 N C Y 428 N C Y 429 N C Y 430 N C Y 431 N C Y 432 N C Y 433 N C N 434 N O N 435 N H N 436 N H N 437 N H N 438 N H N 439 N H N 440 N H N 441 N H N 442 N H N 443 N H N 444 N H N 445 N H N 446 N N N 447 S C N 448 N C N 449 N O N 450 N C N 451 N C N 452 N C N 453 N O N 454 N H N 455 N H N 456 N H N 457 N H N 458 N H N 459 N H N 460 N H N 461 N H N 462 N H N 463 N N N 464 S C N 465 N C N 466 N O N 467 R C N 468 N O N 469 N C N 470 N O N 471 N H N 472 N H N 473 N H N 474 N H N 475 N H N 476 N H N 477 N H N 478 N H N 479 N H N 480 N N N 481 S C N 482 N C N 483 N O N 484 N C Y 485 N C Y 486 N C Y 487 N C Y 488 N N Y 489 N C Y 490 N C Y 491 N C Y 492 N C Y 493 N C N 494 N O N 495 N H N 496 N H N 497 N H N 498 N H N 499 N H N 500 N H N 501 N H N 502 N H N 503 N H N 504 N H N 505 N H N 506 N H N 507 N N N 508 S C N 509 N C N 510 N O N 511 N C Y 512 N C Y 513 N C Y 514 N C Y 515 N C Y 516 N C Y 517 N C N 518 N O N 519 N O N 520 N H N 521 N H N 522 N H N 523 N H N 524 N H N 525 N H N 526 N H N 527 N H N 528 N H N 529 N H N 530 N H N 531 N N N 532 S C N 533 N C N 534 N O N 535 N C N 536 N C N 537 N C N 538 N O N 539 N H N 540 N H N 541 N H N 542 N H N 543 N H N 544 N H N 545 N H N 546 N H N 547 N H N 548 N H N 549 N H N 1 N doub N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing Y 8 N doub Y 9 N sing Y 10 N sing N 11 N sing Y 12 N doub N 13 N sing Y 14 N sing N 15 N sing Y 16 N doub N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N doub N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N doub N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing Y 57 N doub Y 58 N sing Y 59 N sing N 60 N sing Y 61 N doub N 62 N sing Y 63 N doub N 64 N sing Y 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing Y 80 N doub Y 81 N sing Y 82 N sing N 83 N sing Y 84 N doub N 85 N sing Y 86 N doub N 87 N sing Y 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N doub N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N doub N 114 N sing N 115 N sing N 116 N sing N 117 N doub N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing Y 123 N doub Y 124 N sing Y 125 N sing N 126 N sing Y 127 N doub N 128 N sing Y 129 N sing N 130 N sing Y 131 N doub N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N doub N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N doub N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N doub N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N doub N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N doub N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N doub N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N doub N 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N doub N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N doub N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N doub N 263 N sing N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N doub N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N doub N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N sing N 289 N doub N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N sing N 299 N doub N 300 N sing N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N doub N 309 N sing N 310 N sing N 311 N sing N 312 N sing Y 313 N sing Y 314 N doub Y 315 N doub N 316 N sing Y 317 N sing N 318 N sing Y 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N sing N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N sing N 329 N sing N 330 N sing N 331 N doub N 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N sing N 342 N sing N 343 N sing N 344 N sing N 345 N sing N 346 N sing N 347 N sing N 348 N sing N 349 N sing N 350 N sing N 351 N sing N 352 N doub N 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N sing N 358 N sing N 359 N sing N 360 N sing N 361 N sing N 362 N sing N 363 N sing N 364 N sing N 365 N sing N 366 N sing N 367 N sing N 368 N sing N 369 N sing N 370 N sing N 371 N sing N 372 N sing N 373 N doub N 374 N sing N 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing N 383 N sing N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing N 389 N sing N 390 N sing N 391 N sing N 392 N sing N 393 N sing N 394 N sing N 395 N sing N 396 N sing N 397 N doub N 398 N sing N 399 N sing N 400 N sing N 401 N sing N 402 N sing N 403 N sing N 404 N sing N 405 N sing N 406 N sing N 407 N sing N 408 N sing N 409 N sing N 410 N sing N 411 N sing N 412 N sing N 413 N sing N 414 N sing N 415 N sing N 416 N doub N 417 N sing N 418 N sing N 419 N sing N 420 N sing Y 421 N doub Y 422 N sing Y 423 N sing N 424 N sing Y 425 N doub N 426 N sing Y 427 N doub N 428 N sing Y 429 N sing N 430 N sing N 431 N sing N 432 N sing N 433 N sing N 434 N sing N 435 N sing N 436 N sing N 437 N sing N 438 N sing N 439 N doub N 440 N sing N 441 N sing N 442 N sing N 443 N sing N 444 N sing N 445 N sing N 446 N sing N 447 N sing N 448 N sing N 449 N sing N 450 N sing N 451 N sing N 452 N sing N 453 N sing N 454 N sing N 455 N sing N 456 N doub N 457 N sing N 458 N sing N 459 N sing N 460 N sing N 461 N sing N 462 N sing N 463 N sing N 464 N sing N 465 N sing N 466 N sing N 467 N sing N 468 N sing N 469 N sing N 470 N sing N 471 N sing N 472 N doub N 473 N sing N 474 N sing N 475 N sing N 476 N sing Y 477 N doub Y 478 N sing Y 479 N sing N 480 N sing Y 481 N doub Y 482 N sing Y 483 N sing N 484 N sing Y 485 N sing Y 486 N doub N 487 N sing Y 488 N doub N 489 N sing Y 490 N sing N 491 N sing N 492 N sing N 493 N sing N 494 N sing N 495 N sing N 496 N sing N 497 N sing N 498 N sing N 499 N sing N 500 N doub N 501 N sing N 502 N sing N 503 N sing N 504 N sing Y 505 N doub Y 506 N sing Y 507 N sing N 508 N sing Y 509 N doub N 510 N sing Y 511 N doub N 512 N sing Y 513 N sing N 514 N sing N 515 N sing N 516 N sing N 517 N sing N 518 N sing N 519 N sing N 520 N sing N 521 N sing N 522 N sing N 523 N sing N 524 N doub N 525 N sing N 526 N sing N 527 N sing N 528 N sing N 529 N sing N 530 N sing N 531 N sing N 532 N sing N 533 N sing N 534 N sing N 535 N sing US Chem.Biol.Drug Des. 1747-0277 75 257 268 10.1111/j.1747-0285.2009.00943.x 20659109 Fragment-based screen against HIV protease. 2010 10.2210/pdb3kfn/pdb pdb_00003kfn 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 100 1 Rh coated flat mirror CCD 2009-04-17 ADSC QUANTUM 315r Side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg. SINGLE WAVELENGTH M x-ray 1 0.97946 1.0 BL7-1 SSRL 0.97946 SYNCHROTRON SSRL BEAMLINE BL7-1 10831.833 Protease 3.4.23.16 2 man polymer 909.077 benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate 1 syn non-polymer 114.185 (1S,2S)-2-methylcyclohexanol 1 syn non-polymer 78.133 DIMETHYL SULFOXIDE 4 syn non-polymer 39.098 POTASSIUM ION 2 syn non-polymer 78.133 BETA-MERCAPTOETHANOL 1 syn non-polymer 18.015 water 201 nat water no no PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF A,B polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n R8 sample POL 11676 Human immunodeficiency virus 1 562 Escherichia coli BL21.DE3 PLASMID PET 21A+ 1 2.71 54.55 VAPOR DIFFUSION 7.0 0.5 M KSCN, 0.1 M MES-HCL, pH 7.0, 10% DMSO, VAPOR DIFFUSION, temperature 277K 277 database_2 pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site chem_comp_atom chem_comp_bond pdbx_initial_refinement_model repository Initial release Atomic model Database references Derived calculations Non-polymer description Structure summary Version format compliance Other Database references Derived calculations Data collection Refinement description 1 0 2010-02-23 1 1 2011-07-13 1 2 2013-02-27 1 3 2021-10-13 1 4 2023-09-06 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id HIV-1 PROTEASE NL4-3 IN COMPLEX WITH INHIBITOR, TL-3, WILD TYPE HIV Protease with fragment 4D9 bound HIV Protease (PR) dimer without inhibitor; acetate in exo site HIV Protease (PR) with inhibitor TL-3 bound, and DMSOs in exo site HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 1F1 in the outside/top of flap HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 2F4 in the outside/top of flap RCSB Y RCSB 2009-10-27 REL REL 3TL benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate 4DX (1S,2S)-2-methylcyclohexanol DMS DIMETHYL SULFOXIDE K POTASSIUM ION BME BETA-MERCAPTOETHANOL HOH water THE INHIBITOR IS A C2 SYMMETRIC HIV PROTEASE 2AZ8 HIV PR dimer generated from PDB entry 2AZ8 PDB experimental model Inhibitor N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide Peptide-like 3TL 200 2 3TL 3TL 200 A 4DX 201 3 4DX 4DX 201 A DMS 303 4 DMS DMS 303 A DMS 304 4 DMS DMS 304 A DMS 305 4 DMS DMS 305 A K 307 5 K K 307 A BME 300 6 BME BME 300 B DMS 302 4 DMS DMS 302 B K 306 5 K K 306 B HOH 303 7 HOH HOH 204 A HOH 205 7 HOH HOH 205 A HOH 206 7 HOH HOH 206 A HOH 305 7 HOH HOH 207 A HOH 209 7 HOH HOH 209 A HOH 213 7 HOH HOH 213 A HOH 214 7 HOH HOH 214 A HOH 215 7 HOH HOH 215 A HOH 217 7 HOH HOH 217 A HOH 218 7 HOH HOH 218 A HOH 219 7 HOH HOH 219 A HOH 223 7 HOH HOH 223 A HOH 224 7 HOH HOH 224 A HOH 226 7 HOH HOH 226 A HOH 229 7 HOH HOH 229 A HOH 231 7 HOH HOH 231 A HOH 233 7 HOH HOH 233 A HOH 235 7 HOH HOH 235 A HOH 238 7 HOH HOH 238 A HOH 240 7 HOH HOH 240 A HOH 242 7 HOH HOH 242 A HOH 249 7 HOH HOH 249 A HOH 250 7 HOH HOH 250 A HOH 252 7 HOH HOH 252 A HOH 256 7 HOH HOH 256 A HOH 258 7 HOH HOH 258 A HOH 259 7 HOH HOH 259 A HOH 260 7 HOH HOH 260 A HOH 263 7 HOH HOH 263 A HOH 266 7 HOH HOH 266 A HOH 268 7 HOH HOH 268 A HOH 271 7 HOH HOH 271 A HOH 273 7 HOH HOH 273 A HOH 276 7 HOH HOH 276 A HOH 279 7 HOH HOH 279 A HOH 281 7 HOH HOH 281 A HOH 282 7 HOH HOH 282 A HOH 285 7 HOH HOH 285 A HOH 287 7 HOH HOH 287 A HOH 288 7 HOH HOH 288 A HOH 289 7 HOH HOH 289 A HOH 290 7 HOH HOH 290 A HOH 292 7 HOH HOH 292 A HOH 294 7 HOH HOH 294 A HOH 295 7 HOH HOH 295 A HOH 296 7 HOH HOH 296 A HOH 298 7 HOH HOH 298 A HOH 301 7 HOH HOH 301 A HOH 311 7 HOH HOH 311 A HOH 312 7 HOH HOH 312 A HOH 313 7 HOH HOH 313 A HOH 316 7 HOH HOH 316 A HOH 317 7 HOH HOH 317 A HOH 318 7 HOH HOH 318 A HOH 321 7 HOH HOH 321 A HOH 323 7 HOH HOH 323 A HOH 325 7 HOH HOH 325 A HOH 327 7 HOH HOH 327 A HOH 329 7 HOH HOH 329 A HOH 330 7 HOH HOH 330 A HOH 334 7 HOH HOH 334 A HOH 335 7 HOH HOH 335 A HOH 337 7 HOH HOH 337 A HOH 338 7 HOH HOH 338 A HOH 339 7 HOH HOH 339 A HOH 342 7 HOH HOH 342 A HOH 347 7 HOH HOH 347 A HOH 349 7 HOH HOH 349 A HOH 351 7 HOH HOH 351 A HOH 352 7 HOH HOH 352 A HOH 353 7 HOH HOH 353 A HOH 355 7 HOH HOH 355 A HOH 356 7 HOH HOH 356 A HOH 357 7 HOH HOH 357 A HOH 358 7 HOH HOH 358 A HOH 361 7 HOH HOH 361 A HOH 364 7 HOH HOH 364 A HOH 365 7 HOH HOH 365 A HOH 368 7 HOH HOH 368 A HOH 371 7 HOH HOH 371 A HOH 372 7 HOH HOH 372 A HOH 374 7 HOH HOH 374 A HOH 376 7 HOH HOH 376 A HOH 377 7 HOH HOH 377 A HOH 379 7 HOH HOH 379 A HOH 380 7 HOH HOH 380 A HOH 382 7 HOH HOH 382 A HOH 383 7 HOH HOH 383 A HOH 387 7 HOH HOH 387 A HOH 388 7 HOH HOH 388 A HOH 389 7 HOH HOH 389 A HOH 390 7 HOH HOH 390 A HOH 391 7 HOH HOH 391 A HOH 393 7 HOH HOH 393 A HOH 394 7 HOH HOH 394 A HOH 395 7 HOH HOH 395 A HOH 397 7 HOH HOH 397 A HOH 398 7 HOH HOH 398 A HOH 404 7 HOH HOH 404 A HOH 405 7 HOH HOH 405 A HOH 406 7 HOH HOH 406 A HOH 203 7 HOH HOH 203 B HOH 204 7 HOH HOH 204 B HOH 300 7 HOH HOH 205 B HOH 302 7 HOH HOH 206 B HOH 207 7 HOH HOH 207 B HOH 208 7 HOH HOH 208 B HOH 306 7 HOH HOH 209 B HOH 210 7 HOH HOH 210 B HOH 211 7 HOH HOH 211 B HOH 216 7 HOH HOH 216 B HOH 220 7 HOH HOH 220 B HOH 221 7 HOH HOH 221 B HOH 222 7 HOH HOH 222 B HOH 225 7 HOH HOH 225 B HOH 227 7 HOH HOH 227 B HOH 228 7 HOH HOH 228 B HOH 230 7 HOH HOH 230 B HOH 236 7 HOH HOH 236 B HOH 239 7 HOH HOH 239 B HOH 241 7 HOH HOH 241 B HOH 243 7 HOH HOH 243 B HOH 244 7 HOH HOH 244 B HOH 245 7 HOH HOH 245 B HOH 246 7 HOH HOH 246 B HOH 248 7 HOH HOH 248 B HOH 251 7 HOH HOH 251 B HOH 253 7 HOH HOH 253 B HOH 254 7 HOH HOH 254 B HOH 255 7 HOH HOH 255 B HOH 257 7 HOH HOH 257 B HOH 261 7 HOH HOH 261 B HOH 262 7 HOH HOH 262 B HOH 265 7 HOH HOH 265 B HOH 267 7 HOH HOH 267 B HOH 269 7 HOH HOH 269 B HOH 270 7 HOH HOH 270 B HOH 272 7 HOH HOH 272 B HOH 274 7 HOH HOH 274 B HOH 275 7 HOH HOH 275 B HOH 277 7 HOH HOH 277 B HOH 278 7 HOH HOH 278 B HOH 280 7 HOH HOH 280 B HOH 283 7 HOH HOH 283 B HOH 284 7 HOH HOH 284 B HOH 286 7 HOH HOH 286 B HOH 291 7 HOH HOH 291 B HOH 293 7 HOH HOH 293 B HOH 297 7 HOH HOH 297 B HOH 299 7 HOH HOH 299 B HOH 304 7 HOH HOH 304 B HOH 307 7 HOH HOH 307 B HOH 308 7 HOH HOH 308 B HOH 309 7 HOH HOH 309 B HOH 310 7 HOH HOH 310 B HOH 314 7 HOH HOH 314 B HOH 315 7 HOH HOH 315 B HOH 319 7 HOH HOH 319 B HOH 320 7 HOH HOH 320 B HOH 322 7 HOH HOH 322 B HOH 324 7 HOH HOH 324 B HOH 326 7 HOH HOH 326 B HOH 328 7 HOH HOH 328 B HOH 331 7 HOH HOH 331 B HOH 332 7 HOH HOH 332 B HOH 333 7 HOH HOH 333 B HOH 336 7 HOH HOH 336 B HOH 340 7 HOH HOH 340 B HOH 341 7 HOH HOH 341 B HOH 343 7 HOH HOH 343 B HOH 344 7 HOH HOH 344 B HOH 345 7 HOH HOH 345 B HOH 346 7 HOH HOH 346 B HOH 348 7 HOH HOH 348 B HOH 350 7 HOH HOH 350 B HOH 354 7 HOH HOH 354 B HOH 359 7 HOH HOH 359 B HOH 360 7 HOH HOH 360 B HOH 362 7 HOH HOH 362 B HOH 363 7 HOH HOH 363 B HOH 366 7 HOH HOH 366 B HOH 367 7 HOH HOH 367 B HOH 369 7 HOH HOH 369 B HOH 370 7 HOH HOH 370 B HOH 373 7 HOH HOH 373 B HOH 375 7 HOH HOH 375 B HOH 378 7 HOH HOH 378 B HOH 381 7 HOH HOH 381 B HOH 384 7 HOH HOH 384 B HOH 385 7 HOH HOH 385 B HOH 386 7 HOH HOH 386 B HOH 392 7 HOH HOH 392 B HOH 396 7 HOH HOH 396 B HOH 399 7 HOH HOH 399 B HOH 400 7 HOH HOH 400 B HOH 401 7 HOH HOH 401 B HOH 402 7 HOH HOH 402 B HOH 403 7 HOH HOH 403 B HOH 407 7 HOH HOH 407 B HOH 408 7 HOH HOH 408 B HOH 409 7 HOH HOH 409 B PRO 1 n 1 PRO 1 A GLN 2 n 2 GLN 2 A ILE 3 n 3 ILE 3 A THR 4 n 4 THR 4 A LEU 5 n 5 LEU 5 A TRP 6 n 6 TRP 6 A LYS 7 n 7 LYS 7 A ARG 8 n 8 ARG 8 A PRO 9 n 9 PRO 9 A LEU 10 n 10 LEU 10 A VAL 11 n 11 VAL 11 A THR 12 n 12 THR 12 A ILE 13 n 13 ILE 13 A LYS 14 n 14 LYS 14 A ILE 15 n 15 ILE 15 A GLY 16 n 16 GLY 16 A GLY 17 n 17 GLY 17 A GLN 18 n 18 GLN 18 A LEU 19 n 19 LEU 19 A LYS 20 n 20 LYS 20 A GLU 21 n 21 GLU 21 A ALA 22 n 22 ALA 22 A LEU 23 n 23 LEU 23 A LEU 24 n 24 LEU 24 A ASP 25 n 25 ASP 25 A THR 26 n 26 THR 26 A GLY 27 n 27 GLY 27 A ALA 28 n 28 ALA 28 A ASP 29 n 29 ASP 29 A ASP 30 n 30 ASP 30 A THR 31 n 31 THR 31 A VAL 32 n 32 VAL 32 A LEU 33 n 33 LEU 33 A GLU 34 n 34 GLU 34 A GLU 35 n 35 GLU 35 A MET 36 n 36 MET 36 A ASN 37 n 37 ASN 37 A LEU 38 n 38 LEU 38 A PRO 39 n 39 PRO 39 A GLY 40 n 40 GLY 40 A ARG 41 n 41 ARG 41 A TRP 42 n 42 TRP 42 A LYS 43 n 43 LYS 43 A PRO 44 n 44 PRO 44 A LYS 45 n 45 LYS 45 A MET 46 n 46 MET 46 A ILE 47 n 47 ILE 47 A GLY 48 n 48 GLY 48 A GLY 49 n 49 GLY 49 A ILE 50 n 50 ILE 50 A GLY 51 n 51 GLY 51 A GLY 52 n 52 GLY 52 A PHE 53 n 53 PHE 53 A ILE 54 n 54 ILE 54 A LYS 55 n 55 LYS 55 A VAL 56 n 56 VAL 56 A ARG 57 n 57 ARG 57 A GLN 58 n 58 GLN 58 A TYR 59 n 59 TYR 59 A ASP 60 n 60 ASP 60 A GLN 61 n 61 GLN 61 A ILE 62 n 62 ILE 62 A LEU 63 n 63 LEU 63 A ILE 64 n 64 ILE 64 A GLU 65 n 65 GLU 65 A ILE 66 n 66 ILE 66 A CYS 67 n 67 CYS 67 A GLY 68 n 68 GLY 68 A HIS 69 n 69 HIS 69 A LYS 70 n 70 LYS 70 A ALA 71 n 71 ALA 71 A ILE 72 n 72 ILE 72 A GLY 73 n 73 GLY 73 A THR 74 n 74 THR 74 A VAL 75 n 75 VAL 75 A LEU 76 n 76 LEU 76 A VAL 77 n 77 VAL 77 A GLY 78 n 78 GLY 78 A PRO 79 n 79 PRO 79 A THR 80 n 80 THR 80 A PRO 81 n 81 PRO 81 A VAL 82 n 82 VAL 82 A ASN 83 n 83 ASN 83 A ILE 84 n 84 ILE 84 A ILE 85 n 85 ILE 85 A GLY 86 n 86 GLY 86 A ARG 87 n 87 ARG 87 A ASN 88 n 88 ASN 88 A LEU 89 n 89 LEU 89 A LEU 90 n 90 LEU 90 A THR 91 n 91 THR 91 A GLN 92 n 92 GLN 92 A ILE 93 n 93 ILE 93 A GLY 94 n 94 GLY 94 A CYS 95 n 95 CYS 95 A THR 96 n 96 THR 96 A LEU 97 n 97 LEU 97 A ASN 98 n 98 ASN 98 A PHE 99 n 99 PHE 99 A PRO 1 n 1 PRO 1 B GLN 2 n 2 GLN 2 B ILE 3 n 3 ILE 3 B THR 4 n 4 THR 4 B LEU 5 n 5 LEU 5 B TRP 6 n 6 TRP 6 B LYS 7 n 7 LYS 7 B ARG 8 n 8 ARG 8 B PRO 9 n 9 PRO 9 B LEU 10 n 10 LEU 10 B VAL 11 n 11 VAL 11 B THR 12 n 12 THR 12 B ILE 13 n 13 ILE 13 B LYS 14 n 14 LYS 14 B ILE 15 n 15 ILE 15 B GLY 16 n 16 GLY 16 B GLY 17 n 17 GLY 17 B GLN 18 n 18 GLN 18 B LEU 19 n 19 LEU 19 B LYS 20 n 20 LYS 20 B GLU 21 n 21 GLU 21 B ALA 22 n 22 ALA 22 B LEU 23 n 23 LEU 23 B LEU 24 n 24 LEU 24 B ASP 25 n 25 ASP 25 B THR 26 n 26 THR 26 B GLY 27 n 27 GLY 27 B ALA 28 n 28 ALA 28 B ASP 29 n 29 ASP 29 B ASP 30 n 30 ASP 30 B THR 31 n 31 THR 31 B VAL 32 n 32 VAL 32 B LEU 33 n 33 LEU 33 B GLU 34 n 34 GLU 34 B GLU 35 n 35 GLU 35 B MET 36 n 36 MET 36 B ASN 37 n 37 ASN 37 B LEU 38 n 38 LEU 38 B PRO 39 n 39 PRO 39 B GLY 40 n 40 GLY 40 B ARG 41 n 41 ARG 41 B TRP 42 n 42 TRP 42 B LYS 43 n 43 LYS 43 B PRO 44 n 44 PRO 44 B LYS 45 n 45 LYS 45 B MET 46 n 46 MET 46 B ILE 47 n 47 ILE 47 B GLY 48 n 48 GLY 48 B GLY 49 n 49 GLY 49 B ILE 50 n 50 ILE 50 B GLY 51 n 51 GLY 51 B GLY 52 n 52 GLY 52 B PHE 53 n 53 PHE 53 B ILE 54 n 54 ILE 54 B LYS 55 n 55 LYS 55 B VAL 56 n 56 VAL 56 B ARG 57 n 57 ARG 57 B GLN 58 n 58 GLN 58 B TYR 59 n 59 TYR 59 B ASP 60 n 60 ASP 60 B GLN 61 n 61 GLN 61 B ILE 62 n 62 ILE 62 B LEU 63 n 63 LEU 63 B ILE 64 n 64 ILE 64 B GLU 65 n 65 GLU 65 B ILE 66 n 66 ILE 66 B CYS 67 n 67 CYS 67 B GLY 68 n 68 GLY 68 B HIS 69 n 69 HIS 69 B LYS 70 n 70 LYS 70 B ALA 71 n 71 ALA 71 B ILE 72 n 72 ILE 72 B GLY 73 n 73 GLY 73 B THR 74 n 74 THR 74 B VAL 75 n 75 VAL 75 B LEU 76 n 76 LEU 76 B VAL 77 n 77 VAL 77 B GLY 78 n 78 GLY 78 B PRO 79 n 79 PRO 79 B THR 80 n 80 THR 80 B PRO 81 n 81 PRO 81 B VAL 82 n 82 VAL 82 B ASN 83 n 83 ASN 83 B ILE 84 n 84 ILE 84 B ILE 85 n 85 ILE 85 B GLY 86 n 86 GLY 86 B ARG 87 n 87 ARG 87 B ASN 88 n 88 ASN 88 B LEU 89 n 89 LEU 89 B LEU 90 n 90 LEU 90 B THR 91 n 91 THR 91 B GLN 92 n 92 GLN 92 B ILE 93 n 93 ILE 93 B GLY 94 n 94 GLY 94 B CYS 95 n 95 CYS 95 B THR 96 n 96 THR 96 B LEU 97 n 97 LEU 97 B ASN 98 n 98 ASN 98 B PHE 99 n 99 PHE 99 B author_and_software_defined_assembly PISA 2 dimeric 3510 -23 10000 A GLY 94 A O GLY 94 1_555 A K 307 H K K 1_555 A THR 96 A OG1 THR 96 1_555 102.2 A GLY 94 A O GLY 94 1_555 A K 307 H K K 1_555 A HOH 355 L O HOH 1_555 64.9 A THR 96 A OG1 THR 96 1_555 A K 307 H K K 1_555 A HOH 355 L O HOH 1_555 162.9 A GLY 94 A O GLY 94 1_555 A K 307 H K K 1_555 B ASN 98 B O ASN 98 1_555 72.3 A THR 96 A OG1 THR 96 1_555 A K 307 H K K 1_555 B ASN 98 B O ASN 98 1_555 77.5 A HOH 355 L O HOH 1_555 A K 307 H K K 1_555 B ASN 98 B O ASN 98 1_555 107.2 A GLY 94 A O GLY 94 1_555 A K 307 H K K 1_555 B HOH 239 M O HOH 1_555 85.4 A THR 96 A OG1 THR 96 1_555 A K 307 H K K 1_555 B HOH 239 M O HOH 1_555 92.4 A HOH 355 L O HOH 1_555 A K 307 H K K 1_555 B HOH 239 M O HOH 1_555 75.9 B ASN 98 B O ASN 98 1_555 A K 307 H K K 1_555 B HOH 239 M O HOH 1_555 152.7 A GLY 94 A O GLY 94 1_555 A K 307 H K K 1_555 B HOH 384 M O HOH 1_555 166.5 A THR 96 A OG1 THR 96 1_555 A K 307 H K K 1_555 B HOH 384 M O HOH 1_555 90.1 A HOH 355 L O HOH 1_555 A K 307 H K K 1_555 B HOH 384 M O HOH 1_555 101.9 B ASN 98 B O ASN 98 1_555 A K 307 H K K 1_555 B HOH 384 M O HOH 1_555 116.6 B HOH 239 M O HOH 1_555 A K 307 H K K 1_555 B HOH 384 M O HOH 1_555 88.4 A ASN 98 A O ASN 98 1_555 B K 306 K K K 1_555 B GLY 94 B O GLY 94 1_555 78.3 A ASN 98 A O ASN 98 1_555 B K 306 K K K 1_555 B THR 96 B OG1 THR 96 1_555 75.2 B GLY 94 B O GLY 94 1_555 B K 306 K K K 1_555 B THR 96 B OG1 THR 96 1_555 110.8 A ASN 98 A O ASN 98 1_555 B K 306 K K K 1_555 B HOH 354 M O HOH 1_555 146.9 B GLY 94 B O GLY 94 1_555 B K 306 K K K 1_555 B HOH 354 M O HOH 1_555 69.5 B THR 96 B OG1 THR 96 1_555 B K 306 K K K 1_555 B HOH 354 M O HOH 1_555 108.7 A ASN 98 A O ASN 98 1_555 B K 306 K K K 1_555 B HOH 399 M O HOH 1_555 116.0 B GLY 94 B O GLY 94 1_555 B K 306 K K K 1_555 B HOH 399 M O HOH 1_555 66.4 B THR 96 B OG1 THR 96 1_555 B K 306 K K K 1_555 B HOH 399 M O HOH 1_555 166.5 B HOH 354 M O HOH 1_555 B K 306 K K K 1_555 B HOH 399 M O HOH 1_555 57.8 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A N ILE 3 A N ILE 3 B O LEU 97 B O LEU 97 B O THR 96 B O THR 96 A N ASN 98 A N ASN 98 A N LEU 97 A N LEU 97 B O ILE 3 B O ILE 3 A N LYS 45 A N LYS 45 A O VAL 56 A O VAL 56 A N ARG 57 A N ARG 57 A O VAL 77 A O VAL 77 A O LEU 76 A O LEU 76 A N LEU 33 A N LEU 33 A N VAL 32 A N VAL 32 A O ILE 84 A O ILE 84 A O ILE 85 A O ILE 85 A N LEU 23 A N LEU 23 A O ALA 22 A O ALA 22 A N VAL 11 A N VAL 11 A N LYS 14 A N LYS 14 A O GLU 65 A O GLU 65 B N LYS 43 B N LYS 43 B O GLN 58 B O GLN 58 B N ARG 57 B N ARG 57 B O VAL 77 B O VAL 77 B O LEU 76 B O LEU 76 B N LEU 33 B N LEU 33 B N VAL 32 B N VAL 32 B O ILE 84 B O ILE 84 B O ILE 85 B O ILE 85 B N LEU 23 B N LEU 23 B O LYS 20 B O LYS 20 B N ILE 13 B N ILE 13 B N LYS 14 B N LYS 14 B O GLU 65 B O GLU 65 1 A C18 3TL 200 PLANAR A 1 A C18 3TL 200 PLANAR B 1 A C2 3TL 200 PLANAR A 1 A C2 3TL 200 PLANAR B 1 A C68 3TL 200 PLANAR A 1 A C68 3TL 200 PLANAR B 1 A A O O ALA HOH 28 361 1.72 1 A A OD2 O1 ASP 3TL 25 200 2.17 A 1 A GLU 35 -37.37 125.68 76.23 32.903 18.14 3.680 0.000 0.000 -1.940 0.000 -1.730 0.953 0.928 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY 0.274 0.214 0.217 1.770 48.550 1136 23368 21866 5.200 92.580 1.00 0.50 3.905 0.122 RANDOM 1 THROUGHOUT 0.00 MOLECULAR REPLACEMENT 0.149 0.153 0.800 0.800 1.400 HIV PR dimer generated from PDB entry 2AZ8 MAXIMUM LIKELIHOOD MASK 1.770 48.550 201 1815 96 0 1518 0.023 0.021 1904 1.884 2.027 2899 6.461 7.500 392 42.718 24.815 54 14.318 15.000 288 20.329 15.000 8 0.145 0.200 262 0.007 0.021 2048 1.346 1.500 979 2.217 2.000 1592 3.357 3.000 729 4.955 4.500 709 0.367 0.340 1.816 79 1489 1568 1489 20 91.220 27.9 1.770 48.564 3KFN 23368 21896 0.0 0.0 0.089 0.089 1 3.0 3.4 93.7 0.637 1.77 1.82 1.1 1574 0.637 1 3.4 92.5 refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program 5.5.0072 data extraction PDB help@deposit.rcsb.org June 11, 2008 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.005 data collection Blu-Ice data reduction MOSFLM data scaling SCALA phasing MOLREP HIV Protease (PR) with inhibitor TL-3 and fragment hit 4D9 by soaking 1 N N 1 N N 2 N N 3 N N 4 N N 4 N N 4 N N 5 N N 6 N N 4 N N 5 N N 7 N N 7 N N A GLY 86 A GLY 86 HELX_P A THR 91 A THR 91 1 1 6 B GLY 86 B GLY 86 HELX_P B GLY 94 B GLY 94 1 2 9 metalc 2.882 A GLY 94 A O GLY 94 1_555 A K 307 H K K 1_555 metalc 2.972 A THR 96 A OG1 THR 96 1_555 A K 307 H K K 1_555 metalc 2.734 A ASN 98 A O ASN 98 1_555 B K 306 K K K 1_555 metalc 2.910 A K 307 H K K 1_555 A HOH 355 L O HOH 1_555 metalc 2.972 A K 307 H K K 1_555 B ASN 98 B O ASN 98 1_555 metalc 3.496 A K 307 H K K 1_555 B HOH 239 M O HOH 1_555 metalc 3.319 A K 307 H K K 1_555 B HOH 384 M O HOH 1_555 metalc 2.684 B GLY 94 B O GLY 94 1_555 B K 306 K K K 1_555 metalc 3.057 B THR 96 B OG1 THR 96 1_555 B K 306 K K K 1_555 metalc 2.826 B K 306 K K K 1_555 B HOH 354 M O HOH 1_555 metalc 2.987 B K 306 K K K 1_555 B HOH 399 M O HOH 1_555 HYDROLASE/HYDROLASE INHIBITOR HIV-1, PROTEASE, EXO SITE, Aspartyl protease, HYDROLASE-HYDROLASE INHIBITOR COMPLEX Q903N5_9HIV1 UNP 1 1 Q903N5 PQITLWRRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT PVNIIGRNLLTQIGCTLNF 1 99 3KFN 1 99 Q903N5 A 1 1 99 1 99 3KFN 1 99 Q903N5 B 1 1 99 1 ARG engineered mutation LYS 7 3KFN A Q903N5 UNP 7 7 2 ARG engineered mutation LYS 7 3KFN B Q903N5 UNP 7 7 4 8 8 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel parallel anti-parallel anti-parallel A GLN 2 A GLN 2 A ILE 3 A ILE 3 B THR 96 B THR 96 B ASN 98 B ASN 98 A THR 96 A THR 96 A ASN 98 A ASN 98 B GLN 2 B GLN 2 B ILE 3 B ILE 3 A LYS 43 A LYS 43 A GLY 49 A GLY 49 A GLY 52 A GLY 52 A ILE 66 A ILE 66 A HIS 69 A HIS 69 A VAL 77 A VAL 77 A VAL 32 A VAL 32 A LEU 33 A LEU 33 A ILE 84 A ILE 84 A ILE 85 A ILE 85 A GLN 18 A GLN 18 A LEU 24 A LEU 24 A LEU 10 A LEU 10 A ILE 15 A ILE 15 A GLY 52 A GLY 52 A ILE 66 A ILE 66 B LYS 43 B LYS 43 B GLY 49 B GLY 49 B GLY 52 B GLY 52 B ILE 66 B ILE 66 B HIS 69 B HIS 69 B VAL 77 B VAL 77 B VAL 32 B VAL 32 B LEU 33 B LEU 33 B ILE 84 B ILE 84 B ILE 85 B ILE 85 B GLN 18 B GLN 18 B LEU 24 B LEU 24 B LEU 10 B LEU 10 B ILE 15 B ILE 15 B GLY 52 B GLY 52 B ILE 66 B ILE 66 BINDING SITE FOR RESIDUE 3TL A 200 A 3TL 200 Software 34 BINDING SITE FOR RESIDUE 4DX A 201 A 4DX 201 Software 8 BINDING SITE FOR RESIDUE DMS A 303 A DMS 303 Software 9 BINDING SITE FOR RESIDUE DMS A 304 A DMS 304 Software 4 BINDING SITE FOR RESIDUE DMS A 305 A DMS 305 Software 6 BINDING SITE FOR RESIDUE K A 307 A K 307 Software 4 BINDING SITE FOR RESIDUE BME B 300 B BME 300 Software 6 BINDING SITE FOR RESIDUE DMS B 302 B DMS 302 Software 7 BINDING SITE FOR RESIDUE K B 306 B K 306 Software 5 A TRP 6 A TRP 6 34 4_456 A ARG 8 A ARG 8 34 1_555 A ASP 25 A ASP 25 34 1_555 A GLY 27 A GLY 27 34 1_555 A ALA 28 A ALA 28 34 1_555 A ASP 29 A ASP 29 34 1_555 A ASP 30 A ASP 30 34 1_555 A LYS 45 A LYS 45 34 1_555 A MET 46 A MET 46 34 1_555 A ILE 47 A ILE 47 34 1_555 A GLY 48 A GLY 48 34 1_555 A GLY 49 A GLY 49 34 1_555 A ILE 50 A ILE 50 34 1_555 A PHE 53 A PHE 53 34 1_555 A PRO 81 A PRO 81 34 1_555 A VAL 82 A VAL 82 34 1_555 A ILE 84 A ILE 84 34 1_555 A DMS 303 E DMS 34 1_555 A HOH 358 L HOH 34 1_555 A HOH 364 L HOH 34 1_555 B ARG 8 B ARG 8 34 1_555 B LEU 23 B LEU 23 34 1_555 B ASP 25 B ASP 25 34 1_555 B GLY 27 B GLY 27 34 1_555 B ALA 28 B ALA 28 34 1_555 B ASP 29 B ASP 29 34 1_555 B GLY 48 B GLY 48 34 1_555 B GLY 49 B GLY 49 34 1_555 B ILE 50 B ILE 50 34 1_555 B PHE 53 B PHE 53 34 1_555 B PRO 81 B PRO 81 34 1_555 B VAL 82 B VAL 82 34 1_555 B ILE 84 B ILE 84 34 1_555 B HOH 203 M HOH 34 1_555 A LYS 14 A LYS 14 8 1_555 A ILE 15 A ILE 15 8 1_555 A GLY 16 A GLY 16 8 1_555 A GLY 17 A GLY 17 8 1_555 A LEU 63 A LEU 63 8 1_555 A ILE 64 A ILE 64 8 1_555 A GLU 65 A GLU 65 8 1_555 A HOH 301 L HOH 8 1_555 A TRP 6 A TRP 6 9 4_456 A GLY 49 A GLY 49 9 1_555 A ILE 50 A ILE 50 9 1_555 A GLY 51 A GLY 51 9 1_555 A GLY 52 A GLY 52 9 1_555 A 3TL 200 C 3TL 9 1_555 B ILE 54 B ILE 54 9 1_555 B PRO 79 B PRO 79 9 1_555 B PRO 81 B PRO 81 9 1_555 A GLY 73 A GLY 73 4 1_555 A THR 74 A THR 74 4 1_555 A ASN 88 A ASN 88 4 1_555 B ARG 41 B ARG 41 4 3_546 A ARG 87 A ARG 87 6 1_555 A ASN 88 A ASN 88 6 1_555 A THR 91 A THR 91 6 1_555 B LEU 5 B LEU 5 6 1_555 B TRP 6 B TRP 6 6 1_555 B ARG 41 B ARG 41 6 3_546 A GLY 94 A GLY 94 4 1_555 A THR 96 A THR 96 4 1_555 A HOH 355 L HOH 4 1_555 B ASN 98 B ASN 98 4 1_555 A GLN 18 A GLN 18 6 1_556 A ASN 37 A ASN 37 6 1_556 B THR 12 B THR 12 6 1_555 B GLU 65 B GLU 65 6 1_555 B CYS 67 B CYS 67 6 1_555 B GLY 68 B GLY 68 6 1_555 B LYS 14 B LYS 14 7 1_555 B GLY 16 B GLY 16 7 1_555 B GLY 17 B GLY 17 7 1_555 B LEU 63 B LEU 63 7 1_555 B ILE 64 B ILE 64 7 1_555 B GLU 65 B GLU 65 7 1_555 B LYS 70 B LYS 70 7 1_555 A ASN 98 A ASN 98 5 1_555 B GLY 94 B GLY 94 5 1_555 B THR 96 B THR 96 5 1_555 B HOH 354 M HOH 5 1_555 B HOH 399 M HOH 5 1_555 18 P 21 21 2